pre-game fratley got too close to uncovering kuja's schemes and kuja didn't want to have to cover up a dragon knight's murder in addition to all the other plates he had spinning at the moment. so he wiped away his memories with magic instead and wasn't particularly careful about it. the process was irreversible. on good days fratley barely remembers he had a family.
Fratley’s unfinished plotline is probably the result of limitations of the ps1 and perhaps pressure on the development team to cut out larger story/quest lines for characters in the game, but even without taking all that into account his ending with Freya is still, on its own, tragic and unfulfilling. Even at the very end of the game Frately hasn’t regained all his memories and we still don’t know the cause. There’s some theories that Beatrix is to blame for it but I like your concept of it being Kuja and his magic to wipe Frately’s memories.
It’s interesting that not just the continental map but also the world map have notes from Fratley on them. It’s certainly possible that Fratley traveled to the Outer Continent. Maybe he encountered Kuja while exploring the Mist Continent and followed him to the Desert Palace. We know Kuja was skulking around Alexandria and twirling about in Treno so Fratley could have bumped into him and his evildoings. I could see Fratley actually posing a physical threat to Kuja, simply because Fratley refuses to go down easily, so Kuja gets the man off his back, wiping his memory. Leaving the Burmecian to wander the continent unsure of who he even is.
I just wish we had more about Fratley and thus, more importantly, Freya. The later quarter of the game (from Desert Palace to Ipsen Castle) just doesn't feel as nicely paced, or balanced with character moments, as the first half of the game. I feel like we could have gotten some nice character development for Freya using Burmecia and Frately before heading off to the Desert Palace or before Ipsen’s Castle. I’m pretty sure I’ve said this before but it could have even been a good sidequest. Giving the player the choice to go deeper in Burmecia and Freya after the war. But additionally content wasn’t something the developers could work on or throw in the game willy nilly back in the day and ffix went through so many drafts and editing that the story and game that exists as it does today is exactly what the developers were capable of creating at the time.
If a remake for ffix does exist, or will one day in the future, I will be sitting here with all my limbs crossed that it delves deeper into Fratley to service Freya’s character in order to give her the arc and conclusion she really deserved. And ya know, make Frately a little more relevant for his own sake.
